NM_000478.6(ALPL):c.511C>G (p.His171Asp) AND Hypophosphatasia

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Aug 22, 2023
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV003448556.1

Allele description [Variation Report for NM_000478.6(ALPL):c.511C>G (p.His171Asp)]

NM_000478.6(ALPL):c.511C>G (p.His171Asp)

Gene:

ALPL:alkaline phosphatase, biomineralization associated [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

1p36.12

Genomic location:

Preferred name:

NM_000478.6(ALPL):c.511C>G (p.His171Asp)

HGVS:

NC_000001.11:g.21564079C>G
NG_008940.1:g.59715C>G
NG_008940.2:g.60097C>G
NM_000478.6:c.511C>GMANE SELECT
NM_001127501.4:c.346C>G
NM_001177520.3:c.280C>G
NM_001369803.2:c.511C>G
NM_001369804.2:c.511C>G
NM_001369805.2:c.511C>G
NP_000469.3:p.His171Asp
NP_001120973.2:p.His116Asp
NP_001170991.1:p.His94Asp
NP_001356732.1:p.His171Asp
NP_001356733.1:p.His171Asp
NP_001356734.1:p.His171Asp
NC_000001.10:g.21890572C>G

Protein change:

H116D

Molecular consequence:

NM_000478.6:c.511C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001127501.4:c.346C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001177520.3:c.280C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001369803.2:c.511C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001369804.2:c.511C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001369805.2:c.511C>G - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Name:: Hypophosphatasia
Synonyms:: Phosphoethanol-aminuria
Identifiers:: MONDO: MONDO:0018570; MedGen: C0020630

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004175880	JKU Lab, Dept of Paediatrics, Johannes Kepler University	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Aug 22, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004175880

JKU Lab, Dept of Paediatrics, Johannes Kepler University

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Aug 22, 2023)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	1	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From JKU Lab, Dept of Paediatrics, Johannes Kepler University, SCV004175880.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1		1	not provided	not provided	clinical testing	PubMed (1)

Description

Additional compound c.[511C>G];[406C>T] was reported. Variant c.406C>T was reported pathogenic (2)/likely pathogenic(1) and Uncertain significance(1) in ClinVar

Description

Absent in GnomAD. Further information about the ACMG criteria applied can be looked up in the ALPL gene variant database. https://alplmutationdatabase.jku.at/

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		1	not provided	not provided	not provided

Last Updated: Dec 17, 2023

ClinVar

Relating variation to medicine